With the goal of developing more accurate, efficient, non-invasive and fast diagnostic tools, the use of near-infrared (NIR) light in the range of the second and third biological windows (NIR-II: 1000–1350 nm, NIR-III: 1550–1870 nm) is growing remarkably as it provides the advantages of deeper penetration depth into biological tissues, better image contrast, reduced phototoxicity and photobleaching. Consequently, NIR-based bioimaging has become a quickly emerging field and manifold new NIR-emitting bioprobes have been reported. Classes of materials suggested as potential probes for NIR-to-NIR bioimaging (using NIR light for the excitation and emission) are quite diverse. These include rare-earth based nanoparticles, Group-IV nanostructures (single-walled carbon nanotubes, carbon nanoparticles and more recently Si- or Ge-based nanostructures) as well as Ag, In and Pb chalcogenide quantum dots. This review summarizes and discusses current trends, material merits, and latest developments in NIR-to-NIR bioimaging taking advantage of the region above 1000 nm (i.e. the second and third biological windows). Further consideration will be given to upcoming probe materials emitting in the NIR-I region (700–950 nm), thus do not possess emissions in these two windows, but have high expectations. Overall, the focus is placed on recent discussions concerning the optimal choice of excitation and emission wavelengths for deep-tissue high-resolution optical bioimaging and on fluorescent bioprobes that have successfully been implemented in in vitro and in vivo applications.